It was a single word scrawled on a wall at the Hebrew University of Jerusalem that unlocked something deep inside Inbar Michelzon, two years after she had completed compulsory military service in the Israeli Defence Force.

The word was "occupation". "I really felt like someone was speaking the unspoken," she recalled last week in a Tel Aviv cafe. "It was really shocking to me. There was graffiti saying, 'end the occupation'. And I felt like, OK, now I can talk about what I saw."

Michelzon became one of a handful of former Israeli servicewomen who have spoken out about their military experiences, a move that has brought accusations of betrayal and disloyalty. It is impossible to know how representative their testimonies are, but they provide an alternative picture of the "most moral army in the world", as the IDF describes itself.

Israel is unique in enlisting women at the age of 18 into two years of compulsory military service. The experience can be brutalising for the 10% who serve in the occupied territories, as Michelzon did.

"I left the army with a ticking bomb in my belly," she said. "I felt I saw the backyard of Israel. I saw something that people don't speak about. It's almost like I know a dirty secret of a nation and I need to speak out."

Michelzon, now 29, began her military service in September 2000, just when the second intifada was breaking out. "I joined the army with a very idealistic point of view – I really wanted to serve my country." She was posted to Erez, the crossing between Israel and the Gaza Strip, to work in the radio control room.

"There was a lot of tension, a lot of shootings and suicide bombings," she said. "Little by little you understand the rules of the game. You need to make it hard for the Arabs – that's the main rule – because they are the enemy."

She cited a routine example of a Palestinian woman waiting at the crossing. Michelzon called her officer, asking permission to allow the woman through. She was told to make such a request once the woman had been kept waiting for hours. "I felt very alone in the army. I couldn't talk about the things I felt were misplaced," she said. "I didn't have strong views but I felt uncomfortable about the talk, about soldiers hitting Arabs and laughing. I thought everyone else was normal and I was the one who wasn't. I felt an outsider to the group experience."

At the end of her service, in June 2002, Michelzon said she felt the need to escape and took off to India. "I went through a breakdown little by little," she said. It was only when she returned to enrol in university, and two years of therapy, that she began to consider her "duty" to speak out. She also came across Breaking the Silence, an organisation of army veterans who publish testimonies from former soldiers on life in the occupied territories to stimulate debate about the "moral price" of the occupation.

Michelzon gave evidence to the group and two years ago appeared in a documentary, To See If I'm Smiling, about the experiences of young women in the army. The film, she said, was criticised by all sides. The left focused on "the bad things we did and not on the fact that we wanted to start a discussion. We wanted to put up a mirror and tell Israeli society to look itself in the eyes.

"From the right, the reaction was, why are you doing this to your own people? Do you hate your country? But I did it because I love my country. We had to fight to say we want to talk about the political situation."

The psychological impact of military service on women is undeniable, according to the testimonies of Michelzon and others, particularly those who serve in the occupied territories. "If you want to survive as a woman in the army, you have to be manly," she said. "There is no room for feeling. It's like a competition to see who can be tougher. A lot of the time girls are trying to be more aggressive than the guys."

Her experience is echoed by that of Dana Golan, who served in the West Bank city of Hebron in 2001-02 as one of about 25 women among 300 male soldiers. Like Michelzon, Golan only spoke out after finishing her service. "If I had raised my anxieties, it would have been seen as a weakness," she said.

Golan, now 27, said the "most shaky moment" of her military service came during a search for weapons in a Palestinian home. The family were awoken at 2am by soldiers who "turned their whole house inside out". No weapons were found. The small children of the house were terrified, she recalled. "I thought, what would I feel if I was this four-year-old kid? How would I grow up? At that moment it occurred to me that sometimes we're doing things that just create victims. To be a good occupier, we have to create conflict."

On a separate occasion she witnessed soldiers stealing from a Palestinian electronics shop. She tried to report it, only to be told "there were things I shouldn't interfere with".

She said that she also saw elderly Palestinians being humiliated on the streets, "and I thought these could be my parents or grandparents".

Israel is discomfited by these testimonies, she said, partly because of the universality of military service. "We grew up believing the IDF is the most moral army in the world. Everyone knows people serving in the army. Now when I say we are doing immoral things, I am talking about your sister or your daughter. People do not want to hear."

The IDF is proud that 90% of its roles are open equally to men and women. "Serving in a combat unit where you have daily contact with people who might do you harm is not easy – you have to be tough," said Captain Arye Shalicar, an army spokesman. "It's not only a female thing, it's the same for everyone. In the end, a combat unit is a combat unit. Sometimes things happen, not every deed is 100% correct or fair." The army, he said, has procedures for reporting misdeeds which soldiers are encouraged to follow.

Both Michelzon and Golan have no regrets about speaking out. "For two years I saw people suffering and I didn't do anything – and that's really scary," said Michelzon. "At the end, it felt like the army betrayed me – they used me, I couldn't recognise myself. What we call protecting our country is destroying lives."

* Harriet Sherwood is the Guardian's Jerusalem correpondent. She was previously Foreign Editor and Home Editor.